Frequentist GGM

setwd("/Users/ywxiu/Library/CloudStorage/OneDrive-UvA/thesis/R")
library(bootnet)
library(dplyr)
library(EGAnet)
library(qgraph)


# Import data
#dataset is shared on OSF: data.csv
Data <- read.csv2("data.csv",header=T)
Data <- filter(Data, sample == "fr"| sample == "en")
DataFrench <- filter(Data, sample == "fr")
Data <- select(DataFrench,  SBPS1, SBPS2, SBPS3, SBPS4, SBPS5, SBPS6, SBPS7, SBPS8,CEIII1E, CEIII2C, CEIII3E, CEIII4C, CEIII5E, CEIII6C, CEIII7E, CEIII8C, CEIII9E, CEIII10C)

n1 <- EGA(data = Data, model = "glasso", plot.EGA=TRUE)

print(n1)
## Model: GLASSO (EBIC with gamma = 0.5)
## Correlations: auto
## Lambda: 0.0689424853967522 (n = 100, ratio = 0.1)
## 
## Number of nodes: 18
## Number of edges: 80
## Edge density: 0.523
## 
## Non-zero edge weights: 
##      M    SD    Min   Max
##  0.090 0.094 -0.089 0.340
## 
## ----
## 
## Algorithm:  Walktrap
## 
## Number of communities:  2
## 
##    SBPS1    SBPS2    SBPS3    SBPS4    SBPS5    SBPS6    SBPS7    SBPS8 
##        1        1        1        1        1        1        1        1 
##  CEIII1E  CEIII2C  CEIII3E  CEIII4C  CEIII5E  CEIII6C  CEIII7E  CEIII8C 
##        2        2        2        2        2        2        2        2 
##  CEIII9E CEIII10C 
##        2        2 
## 
## ----
## 
## Unidimensional Method: Louvain
## Unidimensional: No
## 
## ----
## 
## TEFI: -14.322
boot.n1 <- bootEGA(data = Data, iter = 1000, typicalStructure = TRUE,
                    plot.typicalStructure = TRUE, model = "glasso", plot.type = "qgraph",
                    type = "parametric", ncores = 2, seed = 1000)

# item and dimension stability
itemStability(boot.n1)

## EGA Type: EGA 
## Bootstrap Samples: 1000 (Parametric)
## 
## Proportion Replicated in Dimensions:
## 
##    SBPS1    SBPS2    SBPS3    SBPS4    SBPS5    SBPS6    SBPS7    SBPS8 
##    1.000    1.000    1.000    1.000    1.000    1.000    1.000    0.921 
##  CEIII1E  CEIII2C  CEIII3E  CEIII4C  CEIII5E  CEIII6C  CEIII7E  CEIII8C 
##    0.997    0.967    0.997    0.992    0.997    0.944    1.000    0.968 
##  CEIII9E CEIII10C 
##    0.997    0.971
dimensionStability(boot.n1)

## EGA Type: EGA 
## Bootstrap Samples: 1000 (Parametric)
## 
## Proportion Replicated in Dimensions:
## 
##    SBPS1    SBPS2    SBPS3    SBPS4    SBPS5    SBPS6    SBPS7    SBPS8 
##    1.000    1.000    1.000    1.000    1.000    1.000    1.000    0.921 
##  CEIII1E  CEIII2C  CEIII3E  CEIII4C  CEIII5E  CEIII6C  CEIII7E  CEIII8C 
##    0.997    0.967    0.997    0.992    0.997    0.944    1.000    0.968 
##  CEIII9E CEIII10C 
##    0.997    0.971 
## 
## ----
## 
## Structural Consistency:
## 
##     1     2 
## 0.942 0.941
EGA.fit(
  data = Data,
  n = NULL,
  uni.method = c("expand", "LE"),
  corr = c("cor_auto", "pearson", "spearman"),
  model = c("glasso", "TMFG"),
  steps = c(3, 4, 5, 6, 7, 8)
)

## Model: GLASSO (EBIC with gamma = 0.5)
## Correlations: auto
## Lambda: 0.0689424853967522 (n = 100, ratio = 0.1)
## 
## Number of nodes: 18
## Number of edges: 80
## Edge density: 0.523
## 
## Non-zero edge weights: 
##      M    SD    Min   Max
##  0.090 0.094 -0.089 0.340
## 
## ----
## 
## Algorithm:  Walktrap (Steps = 3)
## 
## Number of communities:  2
## 
##    SBPS1    SBPS2    SBPS3    SBPS4    SBPS5    SBPS6    SBPS7    SBPS8 
##        1        1        1        1        1        1        1        1 
##  CEIII1E  CEIII2C  CEIII3E  CEIII4C  CEIII5E  CEIII6C  CEIII7E  CEIII8C 
##        2        2        2        2        2        2        2        2 
##  CEIII9E CEIII10C 
##        2        2 
## 
## 
## ----
## 
## TEFI: -14.322
gr<-list('Boredom'=c(1:8),'Curiosity'=c(10,12,14,16,18),'Exploration'= c(9,11,13,15,17))
n1<-estimateNetwork(Data, default= "EBICglasso")
plot(n1, layout = "spring", groups=gr,
             layoutScale = c(1,1), palette = "colorblind",
             theme = "TeamFortress", vsize = 8,legend.cex=0.5)

Bayesian MRF

#Set Working Directory
setwd("/Users/ywxiu/Library/CloudStorage/OneDrive-UvA/thesis/R")

#Load the necessary packages
library(easybgm)
## Registered S3 methods overwritten by 'ergm':
##   method               from 
##   simulate.formula     lme4 
##   simulate.formula_lhs lme4 
##   summary.formula      Hmisc
## Registered S3 methods overwritten by 'BFpack':
##   method               from
##   get_estimates.lm     bain
##   get_estimates.t_test bain
library(bgms)
library(dplyr)

#import data
Data <- read.csv2("data.csv",header=T)
Data <- Data[c(1:490),c(6:13,15:24)]
data <- as.matrix(Data)



#Model fit with easybgm
MRF_fit <- easybgm::easybgm(data = data, 
                            type = "ordinal", 
                            package = "bgms", 
                            interaction_prior="UnitInfo",
                            edge_prior= "Bernoulli",
                            iter = 1e5, 
                            save = TRUE,
                            centrality = TRUE)
MRF_fit0 <- easybgm::easybgm(data = data, 
                            type = "ordinal", 
                            package = "bgms", 
                            interaction_prior="UnitInfo",
                            edge_prior= "Bernoulli",
                            iter = 1e5, 
                            save = FALSE,
                            centrality = TRUE)
#summary output
summary(MRF_fit)
## 
##  BAYESIAN ANALYSIS OF NETWORKS 
##  Model type: ordinal 
##  Number of nodes: 18 
##  Fitting Package: bgms 
## --- 
##  EDGE SPECIFIC OVERVIEW 
##          Relation Estimate Posterior Incl. Prob. Inclusion BF     Category
##       SBPS1-SBPS2    0.133                 1.000          Inf     included
##       SBPS1-SBPS3    0.016                 0.371        0.591 inconclusive
##       SBPS2-SBPS3    0.052                 0.874        6.959 inconclusive
##       SBPS1-SBPS4    0.004                 0.137        0.159 inconclusive
##       SBPS2-SBPS4    0.001                 0.066        0.071     excluded
##       SBPS3-SBPS4    0.005                 0.179        0.218 inconclusive
##       SBPS1-SBPS5    0.110                 1.000          Inf     included
##       SBPS2-SBPS5    0.002                 0.089        0.098     excluded
##       SBPS3-SBPS5    0.129                 1.000          Inf     included
##       SBPS4-SBPS5    0.042                 0.765        3.254 inconclusive
##       SBPS1-SBPS6    0.116                 1.000     2499.000     included
##       SBPS2-SBPS6    0.202                 1.000          Inf     included
##       SBPS3-SBPS6    0.007                 0.178        0.216 inconclusive
##       SBPS4-SBPS6    0.175                 1.000          Inf     included
##       SBPS5-SBPS6    0.091                 0.982       54.066     included
##       SBPS1-SBPS7    0.188                 1.000          Inf     included
##       SBPS2-SBPS7    0.002                 0.078        0.085     excluded
##       SBPS3-SBPS7    0.004                 0.139        0.161 inconclusive
##       SBPS4-SBPS7    0.134                 1.000          Inf     included
##       SBPS5-SBPS7    0.102                 1.000          Inf     included
##       SBPS6-SBPS7    0.046                 0.690        2.222 inconclusive
##       SBPS1-SBPS8   -0.001                 0.058        0.062     excluded
##       SBPS2-SBPS8    0.006                 0.166        0.199 inconclusive
##       SBPS3-SBPS8    0.070                 0.997      309.559     included
##       SBPS4-SBPS8    0.098                 1.000          Inf     included
##       SBPS5-SBPS8    0.001                 0.049        0.051     excluded
##       SBPS6-SBPS8    0.086                 0.994      161.866     included
##       SBPS7-SBPS8   -0.001                 0.051        0.053     excluded
##     SBPS1-CEIII1E    0.000                 0.037        0.039     excluded
##     SBPS2-CEIII1E   -0.053                 0.781        3.561 inconclusive
##     SBPS3-CEIII1E    0.001                 0.058        0.061     excluded
##     SBPS4-CEIII1E    0.000                 0.044        0.046     excluded
##     SBPS5-CEIII1E    0.000                 0.045        0.047     excluded
##     SBPS6-CEIII1E    0.000                 0.044        0.046     excluded
##     SBPS7-CEIII1E   -0.029                 0.509        1.038 inconclusive
##     SBPS8-CEIII1E   -0.001                 0.049        0.052     excluded
##     SBPS1-CEIII2C   -0.002                 0.085        0.093     excluded
##     SBPS2-CEIII2C   -0.017                 0.371        0.591 inconclusive
##     SBPS3-CEIII2C   -0.049                 0.894        8.406 inconclusive
##     SBPS4-CEIII2C    0.002                 0.088        0.096     excluded
##     SBPS5-CEIII2C    0.001                 0.066        0.071     excluded
##     SBPS6-CEIII2C   -0.016                 0.324        0.480 inconclusive
##     SBPS7-CEIII2C    0.002                 0.072        0.077     excluded
##     SBPS8-CEIII2C    0.070                 0.980       49.787     included
##   CEIII1E-CEIII2C   -0.079                 0.974       37.971     included
##     SBPS1-CEIII3E   -0.033                 0.595        1.470 inconclusive
##     SBPS2-CEIII3E    0.003                 0.093        0.102 inconclusive
##     SBPS3-CEIII3E   -0.002                 0.102        0.113 inconclusive
##     SBPS4-CEIII3E    0.009                 0.242        0.319 inconclusive
##     SBPS5-CEIII3E   -0.002                 0.085        0.093     excluded
##     SBPS6-CEIII3E   -0.001                 0.048        0.051     excluded
##     SBPS7-CEIII3E   -0.001                 0.060        0.064     excluded
##     SBPS8-CEIII3E    0.002                 0.077        0.084     excluded
##   CEIII1E-CEIII3E    0.168                 1.000          Inf     included
##   CEIII2C-CEIII3E    0.072                 0.972       34.261     included
##     SBPS1-CEIII4C    0.001                 0.047        0.049     excluded
##     SBPS2-CEIII4C    0.000                 0.040        0.042     excluded
##     SBPS3-CEIII4C    0.000                 0.041        0.043     excluded
##     SBPS4-CEIII4C   -0.001                 0.047        0.049     excluded
##     SBPS5-CEIII4C   -0.001                 0.051        0.053     excluded
##     SBPS6-CEIII4C   -0.010                 0.208        0.263 inconclusive
##     SBPS7-CEIII4C   -0.001                 0.052        0.055     excluded
##     SBPS8-CEIII4C    0.033                 0.568        1.315 inconclusive
##   CEIII1E-CEIII4C    0.090                 0.985       66.659     included
##   CEIII2C-CEIII4C    0.009                 0.215        0.274 inconclusive
##   CEIII3E-CEIII4C    0.000                 0.042        0.044     excluded
##     SBPS1-CEIII5E   -0.079                 0.938       15.116     included
##     SBPS2-CEIII5E   -0.019                 0.347        0.530 inconclusive
##     SBPS3-CEIII5E    0.000                 0.045        0.047     excluded
##     SBPS4-CEIII5E    0.000                 0.044        0.045     excluded
##     SBPS5-CEIII5E   -0.043                 0.676        2.082 inconclusive
##     SBPS6-CEIII5E   -0.056                 0.711        2.462 inconclusive
##     SBPS7-CEIII5E   -0.030                 0.506        1.025 inconclusive
##     SBPS8-CEIII5E   -0.052                 0.809        4.248 inconclusive
##   CEIII1E-CEIII5E    0.093                 0.996      226.790     included
##   CEIII2C-CEIII5E    0.000                 0.042        0.044     excluded
##   CEIII3E-CEIII5E    0.108                 1.000          Inf     included
##   CEIII4C-CEIII5E    0.005                 0.127        0.145 inconclusive
##     SBPS1-CEIII6C    0.000                 0.034        0.036     excluded
##     SBPS2-CEIII6C    0.000                 0.040        0.041     excluded
##     SBPS3-CEIII6C   -0.001                 0.059        0.062     excluded
##     SBPS4-CEIII6C    0.001                 0.060        0.064     excluded
##     SBPS5-CEIII6C    0.000                 0.042        0.044     excluded
##     SBPS6-CEIII6C   -0.001                 0.055        0.058     excluded
##     SBPS7-CEIII6C    0.000                 0.038        0.039     excluded
##     SBPS8-CEIII6C    0.115                 1.000          Inf     included
##   CEIII1E-CEIII6C    0.001                 0.066        0.071     excluded
##   CEIII2C-CEIII6C    0.095                 1.000          Inf     included
##   CEIII3E-CEIII6C    0.009                 0.269        0.369 inconclusive
##   CEIII4C-CEIII6C    0.021                 0.467        0.877 inconclusive
##   CEIII5E-CEIII6C    0.000                 0.042        0.044     excluded
##     SBPS1-CEIII7E    0.023                 0.416        0.712 inconclusive
##     SBPS2-CEIII7E   -0.003                 0.086        0.094     excluded
##     SBPS3-CEIII7E   -0.001                 0.068        0.073     excluded
##     SBPS4-CEIII7E    0.002                 0.077        0.084     excluded
##     SBPS5-CEIII7E   -0.001                 0.048        0.050     excluded
##     SBPS6-CEIII7E    0.002                 0.067        0.072     excluded
##     SBPS7-CEIII7E   -0.059                 0.878        7.227 inconclusive
##     SBPS8-CEIII7E    0.000                 0.040        0.042     excluded
##   CEIII1E-CEIII7E    0.009                 0.201        0.252 inconclusive
##   CEIII2C-CEIII7E    0.088                 1.000     2039.816     included
##   CEIII3E-CEIII7E    0.001                 0.058        0.062     excluded
##   CEIII4C-CEIII7E    0.165                 1.000          Inf     included
##   CEIII5E-CEIII7E    0.043                 0.682        2.148 inconclusive
##   CEIII6C-CEIII7E    0.083                 1.000          Inf     included
##     SBPS1-CEIII8C    0.001                 0.060        0.064     excluded
##     SBPS2-CEIII8C   -0.004                 0.114        0.129 inconclusive
##     SBPS3-CEIII8C   -0.004                 0.140        0.162 inconclusive
##     SBPS4-CEIII8C    0.001                 0.058        0.062     excluded
##     SBPS5-CEIII8C   -0.029                 0.580        1.382 inconclusive
##     SBPS6-CEIII8C    0.000                 0.039        0.040     excluded
##     SBPS7-CEIII8C    0.001                 0.047        0.050     excluded
##     SBPS8-CEIII8C    0.003                 0.096        0.106 inconclusive
##   CEIII1E-CEIII8C    0.038                 0.665        1.987 inconclusive
##   CEIII2C-CEIII8C    0.149                 1.000          Inf     included
##   CEIII3E-CEIII8C    0.092                 1.000          Inf     included
##   CEIII4C-CEIII8C    0.091                 0.998      631.911     included
##   CEIII5E-CEIII8C    0.001                 0.064        0.068     excluded
##   CEIII6C-CEIII8C    0.062                 0.991      115.686     included
##   CEIII7E-CEIII8C    0.001                 0.059        0.062     excluded
##     SBPS1-CEIII9E   -0.051                 0.727        2.663 inconclusive
##     SBPS2-CEIII9E   -0.003                 0.086        0.094     excluded
##     SBPS3-CEIII9E   -0.012                 0.306        0.440 inconclusive
##     SBPS4-CEIII9E    0.003                 0.100        0.111 inconclusive
##     SBPS5-CEIII9E   -0.002                 0.073        0.078     excluded
##     SBPS6-CEIII9E   -0.027                 0.407        0.688 inconclusive
##     SBPS7-CEIII9E   -0.005                 0.136        0.157 inconclusive
##     SBPS8-CEIII9E   -0.004                 0.114        0.128 inconclusive
##   CEIII1E-CEIII9E    0.084                 0.981       51.715     included
##   CEIII2C-CEIII9E    0.001                 0.052        0.054     excluded
##   CEIII3E-CEIII9E    0.006                 0.157        0.186 inconclusive
##   CEIII4C-CEIII9E    0.085                 0.985       64.274     included
##   CEIII5E-CEIII9E    0.099                 0.993      133.048     included
##   CEIII6C-CEIII9E   -0.079                 1.000          Inf     included
##   CEIII7E-CEIII9E    0.253                 1.000          Inf     included
##   CEIII8C-CEIII9E    0.001                 0.043        0.045     excluded
##    SBPS1-CEIII10C   -0.001                 0.051        0.054     excluded
##    SBPS2-CEIII10C   -0.003                 0.097        0.108 inconclusive
##    SBPS3-CEIII10C   -0.001                 0.049        0.051     excluded
##    SBPS4-CEIII10C   -0.005                 0.165        0.197 inconclusive
##    SBPS5-CEIII10C   -0.007                 0.191        0.236 inconclusive
##    SBPS6-CEIII10C    0.000                 0.039        0.040     excluded
##    SBPS7-CEIII10C   -0.001                 0.062        0.066     excluded
##    SBPS8-CEIII10C   -0.003                 0.117        0.133 inconclusive
##  CEIII1E-CEIII10C   -0.015                 0.345        0.526 inconclusive
##  CEIII2C-CEIII10C    0.100                 1.000          Inf     included
##  CEIII3E-CEIII10C   -0.002                 0.075        0.081     excluded
##  CEIII4C-CEIII10C    0.093                 1.000          Inf     included
##  CEIII5E-CEIII10C    0.112                 1.000          Inf     included
##  CEIII6C-CEIII10C    0.000                 0.041        0.043     excluded
##  CEIII7E-CEIII10C    0.000                 0.043        0.045     excluded
##  CEIII8C-CEIII10C    0.073                 0.993      142.062     included
##  CEIII9E-CEIII10C   -0.001                 0.054        0.057     excluded
## 
##  Bayes Factors larger than 10 were considered sufficient evidence for the classification 
##  --- 
##  AGGREGATED EDGE OVERVIEW 
##  Number of edges with sufficient evidence for inclusion: 39 
##  Number of edges with insufficient evidence: 50 
##  Number of edges with sufficient evidence for exclusion: 64 
##  Number of possible edges: 153 
##  
##  --- 
##  STRUCTURE OVERVIEW 
##  Number of visited structures: 99604 
##  Number of possible structures: 1.141798e+46 
##  Posterior probability of most likely structure: 3e-05 
## ---
#Summary method for easybgm objects
summary(MRF_fit, evidence_thresh = 10)
## 
##  BAYESIAN ANALYSIS OF NETWORKS 
##  Model type: ordinal 
##  Number of nodes: 18 
##  Fitting Package: bgms 
## --- 
##  EDGE SPECIFIC OVERVIEW 
##          Relation Estimate Posterior Incl. Prob. Inclusion BF     Category
##       SBPS1-SBPS2    0.133                 1.000          Inf     included
##       SBPS1-SBPS3    0.016                 0.371        0.591 inconclusive
##       SBPS2-SBPS3    0.052                 0.874        6.959 inconclusive
##       SBPS1-SBPS4    0.004                 0.137        0.159 inconclusive
##       SBPS2-SBPS4    0.001                 0.066        0.071     excluded
##       SBPS3-SBPS4    0.005                 0.179        0.218 inconclusive
##       SBPS1-SBPS5    0.110                 1.000          Inf     included
##       SBPS2-SBPS5    0.002                 0.089        0.098     excluded
##       SBPS3-SBPS5    0.129                 1.000          Inf     included
##       SBPS4-SBPS5    0.042                 0.765        3.254 inconclusive
##       SBPS1-SBPS6    0.116                 1.000     2499.000     included
##       SBPS2-SBPS6    0.202                 1.000          Inf     included
##       SBPS3-SBPS6    0.007                 0.178        0.216 inconclusive
##       SBPS4-SBPS6    0.175                 1.000          Inf     included
##       SBPS5-SBPS6    0.091                 0.982       54.066     included
##       SBPS1-SBPS7    0.188                 1.000          Inf     included
##       SBPS2-SBPS7    0.002                 0.078        0.085     excluded
##       SBPS3-SBPS7    0.004                 0.139        0.161 inconclusive
##       SBPS4-SBPS7    0.134                 1.000          Inf     included
##       SBPS5-SBPS7    0.102                 1.000          Inf     included
##       SBPS6-SBPS7    0.046                 0.690        2.222 inconclusive
##       SBPS1-SBPS8   -0.001                 0.058        0.062     excluded
##       SBPS2-SBPS8    0.006                 0.166        0.199 inconclusive
##       SBPS3-SBPS8    0.070                 0.997      309.559     included
##       SBPS4-SBPS8    0.098                 1.000          Inf     included
##       SBPS5-SBPS8    0.001                 0.049        0.051     excluded
##       SBPS6-SBPS8    0.086                 0.994      161.866     included
##       SBPS7-SBPS8   -0.001                 0.051        0.053     excluded
##     SBPS1-CEIII1E    0.000                 0.037        0.039     excluded
##     SBPS2-CEIII1E   -0.053                 0.781        3.561 inconclusive
##     SBPS3-CEIII1E    0.001                 0.058        0.061     excluded
##     SBPS4-CEIII1E    0.000                 0.044        0.046     excluded
##     SBPS5-CEIII1E    0.000                 0.045        0.047     excluded
##     SBPS6-CEIII1E    0.000                 0.044        0.046     excluded
##     SBPS7-CEIII1E   -0.029                 0.509        1.038 inconclusive
##     SBPS8-CEIII1E   -0.001                 0.049        0.052     excluded
##     SBPS1-CEIII2C   -0.002                 0.085        0.093     excluded
##     SBPS2-CEIII2C   -0.017                 0.371        0.591 inconclusive
##     SBPS3-CEIII2C   -0.049                 0.894        8.406 inconclusive
##     SBPS4-CEIII2C    0.002                 0.088        0.096     excluded
##     SBPS5-CEIII2C    0.001                 0.066        0.071     excluded
##     SBPS6-CEIII2C   -0.016                 0.324        0.480 inconclusive
##     SBPS7-CEIII2C    0.002                 0.072        0.077     excluded
##     SBPS8-CEIII2C    0.070                 0.980       49.787     included
##   CEIII1E-CEIII2C   -0.079                 0.974       37.971     included
##     SBPS1-CEIII3E   -0.033                 0.595        1.470 inconclusive
##     SBPS2-CEIII3E    0.003                 0.093        0.102 inconclusive
##     SBPS3-CEIII3E   -0.002                 0.102        0.113 inconclusive
##     SBPS4-CEIII3E    0.009                 0.242        0.319 inconclusive
##     SBPS5-CEIII3E   -0.002                 0.085        0.093     excluded
##     SBPS6-CEIII3E   -0.001                 0.048        0.051     excluded
##     SBPS7-CEIII3E   -0.001                 0.060        0.064     excluded
##     SBPS8-CEIII3E    0.002                 0.077        0.084     excluded
##   CEIII1E-CEIII3E    0.168                 1.000          Inf     included
##   CEIII2C-CEIII3E    0.072                 0.972       34.261     included
##     SBPS1-CEIII4C    0.001                 0.047        0.049     excluded
##     SBPS2-CEIII4C    0.000                 0.040        0.042     excluded
##     SBPS3-CEIII4C    0.000                 0.041        0.043     excluded
##     SBPS4-CEIII4C   -0.001                 0.047        0.049     excluded
##     SBPS5-CEIII4C   -0.001                 0.051        0.053     excluded
##     SBPS6-CEIII4C   -0.010                 0.208        0.263 inconclusive
##     SBPS7-CEIII4C   -0.001                 0.052        0.055     excluded
##     SBPS8-CEIII4C    0.033                 0.568        1.315 inconclusive
##   CEIII1E-CEIII4C    0.090                 0.985       66.659     included
##   CEIII2C-CEIII4C    0.009                 0.215        0.274 inconclusive
##   CEIII3E-CEIII4C    0.000                 0.042        0.044     excluded
##     SBPS1-CEIII5E   -0.079                 0.938       15.116     included
##     SBPS2-CEIII5E   -0.019                 0.347        0.530 inconclusive
##     SBPS3-CEIII5E    0.000                 0.045        0.047     excluded
##     SBPS4-CEIII5E    0.000                 0.044        0.045     excluded
##     SBPS5-CEIII5E   -0.043                 0.676        2.082 inconclusive
##     SBPS6-CEIII5E   -0.056                 0.711        2.462 inconclusive
##     SBPS7-CEIII5E   -0.030                 0.506        1.025 inconclusive
##     SBPS8-CEIII5E   -0.052                 0.809        4.248 inconclusive
##   CEIII1E-CEIII5E    0.093                 0.996      226.790     included
##   CEIII2C-CEIII5E    0.000                 0.042        0.044     excluded
##   CEIII3E-CEIII5E    0.108                 1.000          Inf     included
##   CEIII4C-CEIII5E    0.005                 0.127        0.145 inconclusive
##     SBPS1-CEIII6C    0.000                 0.034        0.036     excluded
##     SBPS2-CEIII6C    0.000                 0.040        0.041     excluded
##     SBPS3-CEIII6C   -0.001                 0.059        0.062     excluded
##     SBPS4-CEIII6C    0.001                 0.060        0.064     excluded
##     SBPS5-CEIII6C    0.000                 0.042        0.044     excluded
##     SBPS6-CEIII6C   -0.001                 0.055        0.058     excluded
##     SBPS7-CEIII6C    0.000                 0.038        0.039     excluded
##     SBPS8-CEIII6C    0.115                 1.000          Inf     included
##   CEIII1E-CEIII6C    0.001                 0.066        0.071     excluded
##   CEIII2C-CEIII6C    0.095                 1.000          Inf     included
##   CEIII3E-CEIII6C    0.009                 0.269        0.369 inconclusive
##   CEIII4C-CEIII6C    0.021                 0.467        0.877 inconclusive
##   CEIII5E-CEIII6C    0.000                 0.042        0.044     excluded
##     SBPS1-CEIII7E    0.023                 0.416        0.712 inconclusive
##     SBPS2-CEIII7E   -0.003                 0.086        0.094     excluded
##     SBPS3-CEIII7E   -0.001                 0.068        0.073     excluded
##     SBPS4-CEIII7E    0.002                 0.077        0.084     excluded
##     SBPS5-CEIII7E   -0.001                 0.048        0.050     excluded
##     SBPS6-CEIII7E    0.002                 0.067        0.072     excluded
##     SBPS7-CEIII7E   -0.059                 0.878        7.227 inconclusive
##     SBPS8-CEIII7E    0.000                 0.040        0.042     excluded
##   CEIII1E-CEIII7E    0.009                 0.201        0.252 inconclusive
##   CEIII2C-CEIII7E    0.088                 1.000     2039.816     included
##   CEIII3E-CEIII7E    0.001                 0.058        0.062     excluded
##   CEIII4C-CEIII7E    0.165                 1.000          Inf     included
##   CEIII5E-CEIII7E    0.043                 0.682        2.148 inconclusive
##   CEIII6C-CEIII7E    0.083                 1.000          Inf     included
##     SBPS1-CEIII8C    0.001                 0.060        0.064     excluded
##     SBPS2-CEIII8C   -0.004                 0.114        0.129 inconclusive
##     SBPS3-CEIII8C   -0.004                 0.140        0.162 inconclusive
##     SBPS4-CEIII8C    0.001                 0.058        0.062     excluded
##     SBPS5-CEIII8C   -0.029                 0.580        1.382 inconclusive
##     SBPS6-CEIII8C    0.000                 0.039        0.040     excluded
##     SBPS7-CEIII8C    0.001                 0.047        0.050     excluded
##     SBPS8-CEIII8C    0.003                 0.096        0.106 inconclusive
##   CEIII1E-CEIII8C    0.038                 0.665        1.987 inconclusive
##   CEIII2C-CEIII8C    0.149                 1.000          Inf     included
##   CEIII3E-CEIII8C    0.092                 1.000          Inf     included
##   CEIII4C-CEIII8C    0.091                 0.998      631.911     included
##   CEIII5E-CEIII8C    0.001                 0.064        0.068     excluded
##   CEIII6C-CEIII8C    0.062                 0.991      115.686     included
##   CEIII7E-CEIII8C    0.001                 0.059        0.062     excluded
##     SBPS1-CEIII9E   -0.051                 0.727        2.663 inconclusive
##     SBPS2-CEIII9E   -0.003                 0.086        0.094     excluded
##     SBPS3-CEIII9E   -0.012                 0.306        0.440 inconclusive
##     SBPS4-CEIII9E    0.003                 0.100        0.111 inconclusive
##     SBPS5-CEIII9E   -0.002                 0.073        0.078     excluded
##     SBPS6-CEIII9E   -0.027                 0.407        0.688 inconclusive
##     SBPS7-CEIII9E   -0.005                 0.136        0.157 inconclusive
##     SBPS8-CEIII9E   -0.004                 0.114        0.128 inconclusive
##   CEIII1E-CEIII9E    0.084                 0.981       51.715     included
##   CEIII2C-CEIII9E    0.001                 0.052        0.054     excluded
##   CEIII3E-CEIII9E    0.006                 0.157        0.186 inconclusive
##   CEIII4C-CEIII9E    0.085                 0.985       64.274     included
##   CEIII5E-CEIII9E    0.099                 0.993      133.048     included
##   CEIII6C-CEIII9E   -0.079                 1.000          Inf     included
##   CEIII7E-CEIII9E    0.253                 1.000          Inf     included
##   CEIII8C-CEIII9E    0.001                 0.043        0.045     excluded
##    SBPS1-CEIII10C   -0.001                 0.051        0.054     excluded
##    SBPS2-CEIII10C   -0.003                 0.097        0.108 inconclusive
##    SBPS3-CEIII10C   -0.001                 0.049        0.051     excluded
##    SBPS4-CEIII10C   -0.005                 0.165        0.197 inconclusive
##    SBPS5-CEIII10C   -0.007                 0.191        0.236 inconclusive
##    SBPS6-CEIII10C    0.000                 0.039        0.040     excluded
##    SBPS7-CEIII10C   -0.001                 0.062        0.066     excluded
##    SBPS8-CEIII10C   -0.003                 0.117        0.133 inconclusive
##  CEIII1E-CEIII10C   -0.015                 0.345        0.526 inconclusive
##  CEIII2C-CEIII10C    0.100                 1.000          Inf     included
##  CEIII3E-CEIII10C   -0.002                 0.075        0.081     excluded
##  CEIII4C-CEIII10C    0.093                 1.000          Inf     included
##  CEIII5E-CEIII10C    0.112                 1.000          Inf     included
##  CEIII6C-CEIII10C    0.000                 0.041        0.043     excluded
##  CEIII7E-CEIII10C    0.000                 0.043        0.045     excluded
##  CEIII8C-CEIII10C    0.073                 0.993      142.062     included
##  CEIII9E-CEIII10C   -0.001                 0.054        0.057     excluded
## 
##  Bayes Factors larger than 10 were considered sufficient evidence for the classification 
##  --- 
##  AGGREGATED EDGE OVERVIEW 
##  Number of edges with sufficient evidence for inclusion: 39 
##  Number of edges with insufficient evidence: 50 
##  Number of edges with sufficient evidence for exclusion: 64 
##  Number of possible edges: 153 
##  
##  --- 
##  STRUCTURE OVERVIEW 
##  Number of visited structures: 99604 
##  Number of possible structures: 1.141798e+46 
##  Posterior probability of most likely structure: 3e-05 
## ---
# =========================
#  DATA VISUALISATION
# =========================

# 0. Plot posterior structure estimates 

# 0.a Posterior structure probability
#Plot Posterior Structure Probabilities
easybgm::plot_structure_probabilities(MRF_fit)

# 0.b. Posterior complexity probability
easybgm::plot_complexity_probabilities(MRF_fit) 

complexity <- c()
for(i in 1:length(MRF_fit$sample_graph)){
  complexity[i] <- sum(as.numeric(unlist(strsplit(MRF_fit$sample_graph[i], ""))))
}

data_complexity <- cbind(complexity, MRF_fit$graph_weights) %>%
  as_tibble() %>% 
  group_by(complexity) %>% 
  summarise(complexity_weight = sum(V2))
## Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if
## `.name_repair` is omitted as of tibble 2.0.0.
## ℹ Using compatibility `.name_repair`.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
data_complexity$complexity
##  [1] 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74
## [26] 75
data_complexity$complexity_weight
##  [1]     8    24    99   331   773  1743  3151  5338  7552 10122 11920 12780
## [13] 11965 10510  8270  6141  4011  2373  1474   777   356   178    63    23
## [25]    16     2
# 1. Plot structure
#generate 3 groups in plot
generate_sequence <- function() {
  sequence <- character(0)
  for (i in 1:10) {
    if (i %% 2 == 0) {
      sequence <- c(sequence, "Curiosity")
    } else {
      sequence <- c(sequence, "Exploration")
    }
  }
  return(sequence)
}
result <- generate_sequence()
Groups <- c(rep("Boredom Proneness", 8), result)

easybgm::plot_structure(MRF_fit, layoutScale = c(.8,1), palette = "colorblind",legend = F, groups = Groups,
               theme = "TeamFortress", vsize = 6, edge.width = .3, layout = "spring")

# 2. Plot network model (also referred to as median probability model)
# set two plots with the same layout.
Layout <- qgraph::averageLayout(n1)
easybgm::plot_network(MRF_fit, layout = Layout, groups=Groups,legend=F,
             layoutScale = c(1,1), palette = "colorblind",
             theme = "TeamFortress", vsize = 8,evidence_thresh = 10,dashed = TRUE)

# 3. Plot evidence plot
easybgm::plot_edgeevidence(MRF_fit, split = T,edge.width = 2,evidence_thresh = 10,groups=Groups,legend=F,palette = "colorblind",layout=Layout)

## [[1]]
## From     To  Weight
## 1     ---     2   1 
## 2     ---     3   1 
## 1     ---     5   1 
## 3     ---     5   1 
## 4     ---     5   1 
## 1     ---     6   1 
## 2     ---     6   1 
## 4     ---     6   1 
## 5     ---     6   1 
## 1     ---     7   1 
## 4     ---     7   1 
## 5     ---     7   1 
## 6     ---     7   1 
## 3     ---     8   1 
## 4     ---     8   1 
## 6     ---     8   1 
## 2     ---     9   1 
## 7     ---     9   1 
## 3     ---     10      1 
## 8     ---     10      1 
## 9     ---     10      1 
## 1     ---     11      1 
## 9     ---     11      1 
## 10    ---     11      1 
## 8     ---     12      1 
## 9     ---     12      1 
## 1     ---     13      1 
## 5     ---     13      1 
## 6     ---     13      1 
## 7     ---     13      1 
## 8     ---     13      1 
## 9     ---     13      1 
## 11    ---     13      1 
## 8     ---     14      1 
## 10    ---     14      1 
## 7     ---     15      1 
## 10    ---     15      1 
## 12    ---     15      1 
## 13    ---     15      1 
## 14    ---     15      1 
## 5     ---     16      1 
## 9     ---     16      1 
## 10    ---     16      1 
## 11    ---     16      1 
## 12    ---     16      1 
## 14    ---     16      1 
## 1     ---     17      1 
## 9     ---     17      1 
## 12    ---     17      1 
## 13    ---     17      1 
## 14    ---     17      1 
## 15    ---     17      1 
## 10    ---     18      1 
## 12    ---     18      1 
## 13    ---     18      1 
## 16    ---     18      1 
## 
## [[2]]
## From     To  Weight
## 1     ---     3   1 
## 1     ---     4   1 
## 2     ---     4   1 
## 3     ---     4   1 
## 2     ---     5   1 
## 3     ---     6   1 
## 2     ---     7   1 
## 3     ---     7   1 
## 1     ---     8   1 
## 2     ---     8   1 
## 5     ---     8   1 
## 7     ---     8   1 
## 1     ---     9   1 
## 3     ---     9   1 
## 4     ---     9   1 
## 5     ---     9   1 
## 6     ---     9   1 
## 8     ---     9   1 
## 1     ---     10      1 
## 2     ---     10      1 
## 4     ---     10      1 
## 5     ---     10      1 
## 6     ---     10      1 
## 7     ---     10      1 
## 2     ---     11      1 
## 3     ---     11      1 
## 4     ---     11      1 
## 5     ---     11      1 
## 6     ---     11      1 
## 7     ---     11      1 
## 8     ---     11      1 
## 1     ---     12      1 
## 2     ---     12      1 
## 3     ---     12      1 
## 4     ---     12      1 
## 5     ---     12      1 
## 6     ---     12      1 
## 7     ---     12      1 
## 10    ---     12      1 
## 11    ---     12      1 
## 2     ---     13      1 
## 3     ---     13      1 
## 4     ---     13      1 
## 10    ---     13      1 
## 12    ---     13      1 
## 1     ---     14      1 
## 2     ---     14      1 
## 3     ---     14      1 
## 4     ---     14      1 
## 5     ---     14      1 
## 6     ---     14      1 
## 7     ---     14      1 
## 9     ---     14      1 
## 11    ---     14      1 
## 12    ---     14      1 
## 13    ---     14      1 
## 1     ---     15      1 
## 2     ---     15      1 
## 3     ---     15      1 
## 4     ---     15      1 
## 5     ---     15      1 
## 6     ---     15      1 
## 8     ---     15      1 
## 9     ---     15      1 
## 11    ---     15      1 
## 1     ---     16      1 
## 2     ---     16      1 
## 3     ---     16      1 
## 4     ---     16      1 
## 6     ---     16      1 
## 7     ---     16      1 
## 8     ---     16      1 
## 13    ---     16      1 
## 15    ---     16      1 
## 2     ---     17      1 
## 3     ---     17      1 
## 4     ---     17      1 
## 5     ---     17      1 
## 6     ---     17      1 
## 7     ---     17      1 
## 8     ---     17      1 
## 10    ---     17      1 
## 11    ---     17      1 
## 16    ---     17      1 
## 1     ---     18      1 
## 2     ---     18      1 
## 3     ---     18      1 
## 4     ---     18      1 
## 5     ---     18      1 
## 6     ---     18      1 
## 7     ---     18      1 
## 8     ---     18      1 
## 9     ---     18      1 
## 11    ---     18      1 
## 14    ---     18      1 
## 15    ---     18      1 
## 17    ---     18      1
# 4. Plot parameter forest plot  
easybgm::plot_parameterHDI(MRF_fit)

# 5. Plot strength centrality estimate and 95% highest density interval 
easybgm::plot_centrality(MRF_fit)